Laboratory Assistant     Suite
PlayersStarting May 2011, LAS stems from the joined efforts of IRCC and the Politecnico of Torino                         ...
GoalsStructured data management• Samples data (biobank)• Biological data (xenos and cell lines)• Molecular data (instrumen...
FeaturesData Entry•   Real-time•   Time saving•   User friendly•   Error proofData Analysis•   Integrative•   Reproducible...
Technical Specs•   Web-based•   Ad-hoc GUIs•   Relational and NOSQL Databases•   Distributed•   Audit trail•   A mnemonic ...
Genealogy ID        Features        •    Unique        •    Intrinsic to key biological entities        •    Encodes relev...
Data Flow                   Tissue                      Aliquots          BIOBANKING OperationTreatments                  ...
LAS data tracking system              Storage                             XenoIntegrative                     Sample      ...
LAS facts&numbersLAS manages (starting April 2012):•   622 surgical samples collection•   7158 mice•   6895 implanted xeno...
LAS modules                 Integrative analysis module                                                                   ...
Current FunctionalitiesBiobank                                      Storage•   Sample collection tracking               • ...
People• IRCC (contributors&users)   • POLITO (developers)  • Eugenia Zanella             staff  •   Giorgia Migliardi     ...
MilestonesThe project is implemented through three steps:Phase I - Biobanking & Xenopatients management•   Storage•   Aliq...
Biobanking Module
Xenografts Module
Query Module
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LAS - Project Overview

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Introduction to Laboratory Assistant Suite

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LAS - Project Overview

  1. 1. Laboratory Assistant Suite
  2. 2. PlayersStarting May 2011, LAS stems from the joined efforts of IRCC and the Politecnico of Torino IRCC contribution • Strategy • Working- and Data-flow analysis • User interface definition • On-site implementation POLITO contribution • Database & Data warehouse • Analytical tools & software features • IT
  3. 3. GoalsStructured data management• Samples data (biobank)• Biological data (xenos and cell lines)• Molecular data (instruments)• Public data (open access databases)Integrative analysis management• Complex queries across multiple databases (including clinical annotations)• Analysis tools• Annotations
  4. 4. FeaturesData Entry• Real-time• Time saving• User friendly• Error proofData Analysis• Integrative• Reproducible• Intuitive• No programming skills required
  5. 5. Technical Specs• Web-based• Ad-hoc GUIs• Relational and NOSQL Databases• Distributed• Audit trail• A mnemonic code (GenID) intrisically represents the most critical attributes of the main biological entities
  6. 6. Genealogy ID Features • Unique • Intrinsic to key biological entities • Encodes relevant information regarding the history of the entity • Automatically generated through formal rules XENOPATIENT ALIQUOT CRC 0001 LM X 0A 01 001 TUM RL0100 Collection type Tissue type Lineage Mouse ID Aliquot type(tumor type, eg colorectal) (eg liver metastasis) (eg tracks the line (individual mouse (eg RNAlater) generation event) number) Collection Event Vector type Passage Explanted Aliquot ID (sequencial) (eg xeno, original (n° of generations Tissue (individual aliquot human or cell line) ex-vivo) (eg number) tumor, lung, liver, et c.)
  7. 7. Data Flow Tissue Aliquots BIOBANKING OperationTreatments Explants Derived Implants Storage Aliquots MouseMeasurements XENOPATIENTSEXPERIMENTSNext Generation Sequecing Molecular Experiments Images
  8. 8. LAS data tracking system Storage XenoIntegrative Sample Mice analyses Containers BIOLOGICAL DATA SurgicalSpecimens LAS LAS Facilities ALIQUOTs XENOs LAS ALIQUOTs TRANSFORMATION EXPANSIONBiobank EVENTS EVENTS MOLECULAR DATA
  9. 9. LAS facts&numbersLAS manages (starting April 2012):• 622 surgical samples collection• 7158 mice• 6895 implanted xenografts• 4790 explanted xenografts• 18537 measures (digital caliper)• 1656 mice treated with 44 different protocols&schedules• 51131 archived aliquots• 3530 derivation events (eg DNA extraction)
  10. 10. LAS modules Integrative analysis module Account and Privilege Manager Integrative Public data Clinical data General facilities STATUSquery module miner miner manager working advanced development intermediate development Biobank uArray Animal early Xeno managementmanagement management imaging development scheduled Storage Cell lines SangerSeq Microscopymanagement management management Animal Animal RT-PCR FACS & Pathology models facility management Beaming
  11. 11. Current FunctionalitiesBiobank Storage• Sample collection tracking • Management of containers• Aliquots Exchange/Split/Usage tracking • Tracking archive process• Support to derivation processes Query (protocols, QC/QA) • Definition of complex queries• Consumables stock usage (Kits) • Integration of heterogeneous dataXenopatients • Exploration of genealogy trees• Mice life cycle tracking Analysis• Surgery practices tracking • Data mining analyses• Tumor growth tracking • Computation of aggregated data• Treatment protocols • Plot of data statistics• Support to decision making process for experiments
  12. 12. People• IRCC (contributors&users) • POLITO (developers) • Eugenia Zanella staff • Giorgia Migliardi • Alessandro Fiori (coordinator) • Francesca Cottino • Alberto Grand • Francesco Galimi • Piero Alberto • Michela Buscarino • Emanuele Geda • Carlo Zanon students • Gabriele Picco • Marco Alaimo • Roberta Porporato • Francesco Brundu • Daniela Cantarella • Maria Cabiati • Tommaso Renzulli • Stefania Mellai • Enzo Medico • Raffaele Passanati • Domenico Schioppa
  13. 13. MilestonesThe project is implemented through three steps:Phase I - Biobanking & Xenopatients management• Storage• Aliquots (tissues & derivatives)• Transformation processes• Mice• In Vivo experimentsPhase II - General facilities management• uArrays• Sanger sequencing• RT-PCR• FACS• Animal Facility (?)Phase III - General purpose data management• In vitro experiments• Imaging• Analytical tools• NextGenSeq data management (in collaboration with informatics)• Mouse models• Clinical data integration
  14. 14. Biobanking Module
  15. 15. Xenografts Module
  16. 16. Query Module

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